After the release of the game, the animal rights group PETA created a website and Flash game called "Mario Kills Tanooki." The game involves a skinless raccoon dog chasing Mario, who is wearing the suit. According to Eurogamer, Nintendo later made a statement saying:

"Mario often takes the appearance of certain animals and objects in his games. These have included a frog, a penguin, a balloon, and even a metallic version of himself. These lighthearted and whimsical transformations give Mario different abilities and make his games fun to play. The different forms that Mario takes make no statement beyond the games themselves."

PETA later stated that the game was "tongue-in-cheek", and intended to draw attention to real issues.

Two alternate HOME screen jingles can be found in the game's files. The first is a shortened version of the one used in the final game, and the second is the first 6 notes of the Super Mario Bros. theme. The latter was reused in Animal Crossing: New Leaf for when the player puts on Mario-related clothing.

While the ending of the Bowser's Message fanfare from Super Mario 64 is used when Mario is shocked by what one of the flying letters has, there's also the first half of the fanfare left unused in the game.

Following the events of the massive earthquake that devastated Japan in March 2011, the development of Super Mario 3D Land shifted focus entirely. Nintendo's primary goal became making a game that could bring happiness to a tragedy-struck country.

World 5-2 is designed in a Legend of Zelda format, using a top-down view, lots of rooms, and no stompable enemies. Also, if you light all of the torches in a certain room using a Fire Flower, a secret door opens and a Zelda sound effect is heard. The level was designed in honor of LoZ's 25th anniversary, hinted at by the level number: "5-2" is "25" backwards.